Extended Data Fig. 2: Analyses of pre-mRNA splicing in grp20 flowers and leaves, as compared to WT.

a, Illustrations of categories of splicing defects observed in this study. The categories are exon skipping (ES); alternative 3’ splicing site (A3SS); alternative 5’ splicing site (A5SS), alternative mutually exclusive exon (aMXE), and alternatively spliced intron (ASI), including intron retention (IR), delayed intron degradation (DID), and alternative exon (AE) inside an intron. The blue and red rectangles represent normal exons, yellow rectangles represent abnormal exonic sequences, and the white rectangles represent introns. b, Numbers of genes/transcripts with ASI and aMXE splicing defects in the flower-specific group and the overlapping group between flower and leaf. c, Numbers of genes/transcripts with ASI and aMXE splicing defects in the leaf-specific group and the overlapping group between leaf and flower. d, A heatmap of defective types and significance of each gene in flowers and leaves. P-values are categorized to two groups: p < 0.01 (blue) and 0.01 ≤ p < 0.05 (dark blue) (a likelihood-ratio test with 95% confidence intervals). The splicing defects are categorized into five groups including ES (light red), A3SS (yellow), A5SS (light green), aMXE (gray), and ASI (light purple). Among the splicing defects specifically detected in floral transcripts, ASI and ES are more frequent than other types. e, A Venn diagram of the overlap between genes in different GO categories. 64 genes in flower development (including petal development, ovule development and floral organ formation), morphogenesis structure and meristem development are highly enriched in defective transcripts in grp20 flowers. f, A Venn diagram of the overlap between defective transcription factor families and enriched defective transcription factor families in flower specific (blue circle), in flower and leaf overlapping (red circle), and in leaf specific (purple circle) groups. g-i, Fractions of all annotated transcription factors containing abnormal transcripts to all transcription factors in the same family in grp20 flower specific (g), leaf specific (h), and flower and leaf overlapping groups (i). The enrichment is compared to referenced fractions of transcription factors in each family to all 1,717 transcription factors. The enriched defects in flower and leaf are defined if the defective fraction is more than referenced fraction. Two asterisks (**) indicate enrichment of defects in corresponding transcription factor family if the defective fraction is more than twice of reference fraction.